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• Karolinska Institutet - Susanne Schlisio Lab

  DAC for Susanne Schlisio Lab, Department of Oncology-Pathology, Karolinska Institutet, Sweden

  Dac EGAC50000000603

• Genomic Sequencing of Triple Negative Breast Cancer - CUTseq data

  CUTseq data for study EGAS00001008261

  Dataset EGAD00001015684

• WES of TGA

  Whole exome sequencing data for 381 TGA probands

  Dataset EGAD00001005809

• NGS sequencing data of archival FFPE tumor tissue

  The aim of the study was to identify mutations in key ovarian cancer genes (BRCA1, BRCA2,TP53, PTEN, ATM, ATR, NF1) in archival fresh-frozen paraffin embedded (FFPE) tumor tissue from platinum-resistant ovarian cancer patients enrolled in the phase I/II GANNET53 clinical trial. From the enrolled 133 patients, archival FFPE tissue was available and DNA was extracted thereof. The DNA samples passing quality control (n=118) were NGS sequenced using the SureSeq™ Ovarian Cancer Panel and the NGS Library Preparation kit (Oxford Gene Technology), which covers all exons of 7 key ovarian cancer genes for single nucleotide variants (SNV) and indels, and the Illumina MiSeq platform. For the paired-end runs, one Read 1 (R1) and one Read 2 (R2) FASTQ file were created for each sample. FASTQ files were compressed and created with the extension \.fastq.gz.

  Dataset EGAD50000001371

• Whole-genome sequences of single-cell derived clonal samples and bulk blood samples from human

  Human single cells were clonally expanded by culture and whole-genome sequenced. This dataset includes 334 clonal samples and 7 blood bulks from seven individuals (DB2, DB3, DB5, DB6, DB8, DB9, DB10). We extracted genomic DNA materials from clonally expanded cells and matched peripheral blood using DNeasy Blood and Tissue kits (Qiagen) according to the protocol. DNA libraries for WGS were generated by an Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) from 1 µg of genomic DNA materials. WGS was performed on either the Illumina HiSeq X platform or the NovaSeq 6000 platform to generate mean coverage of 25.2X for 374 clonally expanded cells and 94.8X for 7 matched blood tissues.

  Dataset EGAD00001007032

• BLUEPRINT release August 2014, ChIP-Seq for CD34-negative, CD41-positive, CD42-positive megakaryocyte cell

  ChIP-Seq data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001000916

• Bulk RNA Sequencing of 86 Human Donor Lungs

  The goal of this study was to characterize the effect of age on gene expression in normal human lung. We collected distal lung samples from 86 human donors distributed in age between 16 and 76 years and extracted RNA for Illumina-based sequencing.

  Study phs002484

• High-grade serous ovarian carcinoma tumour exome sequencing variants

  Tumour variants (in VCF format) from exome sequencing (using Agilent SureSelect and TWIST library preparation systems followed by sequencing on Illumina HiSeq and NovaSeq platforms) of 108 high-grade serous ovarian tumour samples. Germline variants from EGAD00001006030 for these individuals were used to call somatic and tumour-only variants separately, creating two VCF files per sample (except for one sample without paired germline data- somatic variant file only provided). The dataset comprises 215 VCF variant files.

  Dataset EGAD50000001132

• COVID_Methyl_scRNA

  DAC for the study of whole-genome enzymatic DNA methylation sequencing and single-cell RNA sequencing of nasal cells from COVID-19 patients. Nasal swabs were collected from COVID-19 patients during the acute phase of infection as well as 3 and 12-months post-infection. Cells isolated from nasal swabs were subjected to whole-genome enzymatic DNA methylation sequencing (n=33) and scRNA-seq (n=24). For n=12 former COVID-19 pateints, follow-up samples were collected at 3 and 12 months post-infection and subjected to scRNA-seq.

  Dac EGAC50000000197

• Comprehensive molecular profiling with whole-exome sequencing (WES) of PDX tumors

  To identify biomarkers for the antitumor effects of molecularly targeted therapy, we performed whole-exome sequencing on 795 patient-derived xenograft (PDX) samples established from 269 patients with solid tumors and 125 frozen tissue samples obtained at the time of surgery.

  Study JGAS000853